qiime@qiime-190-virtual-box:~/Desktop/Shared_Folder/InSilicoSeq$ iss generate --genomes PV3_gb_MF678293Short.fasta --model miseq --output miseq_reads -n 10000
INFO:iss.app:Starting iss generate
INFO:iss.app:Using kde ErrorModel
INFO:iss.app:Using lognormal abundance distribution
INFO:iss.app:Using 2 cpus for read generation
INFO:iss.app:Generating 10000 reads
INFO:iss.app:Generating reads for record: PV3Test
ERROR:iss.generator:PV3Test shorter than template length for this ErrorModel:empty range for randrange() (0,-33, -33)
ERROR:iss.generator:Skipping this record: PV3Test
Traceback (most recent call last):
  File "/usr/local/bin/iss", line 9, in <module>
    load_entry_point('InSilicoSeq==1.0.0', 'console_scripts', 'iss')()
  File "/usr/local/lib/python2.7/dist-packages/iss/app.py", line 378, in main
    args.func(args)
  File "/usr/local/lib/python2.7/dist-packages/iss/app.py", line 146, in generate_reads
    args.gc_bias) for i in range(cpus))
  File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 789, in __call__
    self.retrieve()
  File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 740, in retrieve
    raise exception
joblib.my_exceptions.JoblibTypeError: JoblibTypeError
___________________________________________________________________________
Multiprocessing exception:
...........................................................................
/usr/local/bin/iss in <module>()
      4 import sys
      5 from pkg_resources import load_entry_point
      6 
      7 if __name__ == '__main__':
      8     sys.exit(
----> 9         load_entry_point('InSilicoSeq==1.0.0', 'console_scripts', 'iss')()
     10     )

...........................................................................
/usr/local/lib/python2.7/dist-packages/iss/app.py in main()
    373         elif args.debug:
    374             logging.basicConfig(level=logging.DEBUG)
    375         else:
    376             logging.basicConfig(level=logging.INFO)
    377 
--> 378         args.func(args)
        args.func = <function generate_reads>
        args = Namespace(abundance='lognormal', abundance_file=...output='miseq_reads', quiet=False, version=False)
    379         logging.shutdown()
    380     except AttributeError as e:
    381         logger = logging.getLogger(__name__)
    382         logger.debug(e)

...........................................................................
/usr/local/lib/python2.7/dist-packages/iss/app.py in generate_reads(args=Namespace(abundance='lognormal', abundance_file=...output='miseq_reads', quiet=False, version=False))
    141 
    142                         record_file_name_list = Parallel(n_jobs=cpus)(
    143                             delayed(generator.reads)(
    144                                 record, err_mod,
    145                                 n_pairs_per_cpu, i, args.output,
--> 146                                 args.gc_bias) for i in range(cpus))
        args.gc_bias = False
        cpus = 2
    147                         temp_file_list.extend(record_file_name_list)
    148         except KeyboardInterrupt as e:
    149             logger.error('iss generate interrupted: %s' % e)
    150             generator.cleanup(temp_file_list)

...........................................................................
/usr/local/lib/python2.7/dist-packages/joblib/parallel.py in __call__(self=Parallel(n_jobs=2), iterable=<generator object <genexpr>>)
    784             if pre_dispatch == "all" or n_jobs == 1:
    785                 # The iterable was consumed all at once by the above for loop.
    786                 # No need to wait for async callbacks to trigger to
    787                 # consumption.
    788                 self._iterating = False
--> 789             self.retrieve()
        self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=2)>
    790             # Make sure that we get a last message telling us we are done
    791             elapsed_time = time.time() - self._start_time
    792             self._print('Done %3i out of %3i | elapsed: %s finished',
    793                         (len(self._output), len(self._output),

---------------------------------------------------------------------------
Sub-process traceback:
---------------------------------------------------------------------------
TypeError                                          Wed Jan 24 08:20:38 2018
PID: 20635                                    Python 2.7.3: /usr/bin/python
...........................................................................
/usr/local/lib/python2.7/dist-packages/joblib/parallel.py in __call__(self=<joblib.parallel.BatchedCalls object>)
    126     def __init__(self, iterator_slice):
    127         self.items = list(iterator_slice)
    128         self._size = len(self.items)
    129 
    130     def __call__(self):
--> 131         return [func(*args, **kwargs) for func, args, kwargs in self.items]
        func = <function reads>
        args = (SeqRecord(seq=Seq('GCCCCTGAATGCGGCTAATCCTAACCATG...ame='PV3Test', description='PV3Test', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 2500, 1, 'miseq_reads', False)
        kwargs = {}
        self.items = [(<function reads>, (SeqRecord(seq=Seq('GCCCCTGAATGCGGCTAATCCTAACCATG...ame='PV3Test', description='PV3Test', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 2500, 1, 'miseq_reads', False), {})]
    132 
    133     def __len__(self):
    134         return self._size
    135 

...........................................................................
/usr/local/lib/python2.7/dist-packages/iss/generator.py in reads(record=SeqRecord(seq=Seq('GCCCCTGAATGCGGCTAATCCTAACCATG...ame='PV3Test', description='PV3Test', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, n_pairs=2500, cpu_number=1, output='miseq_reads', gc_bias=False)
     44         'Cpu #%s: Generating %s read pairs'
     45         % (cpu_number, n_pairs))
     46     read_tuple_list = []
     47     for i in range(n_pairs):
     48         try:
---> 49             forward, reverse = simulate_read(record, ErrorModel, i)
        forward = SeqRecord(seq=Seq('CAACCCAGCAGCCAGCCTGTCGTAACGCG...me='<unknown name>', description=u'', dbxrefs=[])
        reverse = SeqRecord(seq=Seq('GGCTCGGTTAGAATTCTCGTGAGCGCCTA...me='<unknown name>', description=u'', dbxrefs=[])
        record = SeqRecord(seq=Seq('GCCCCTGAATGCGGCTAATCCTAACCATG...ame='PV3Test', description='PV3Test', dbxrefs=[])
        ErrorModel = <iss.error_models.kde.KDErrorModel object>
        i = 5
     50         except ValueError as e:
     51             logger.error('Skipping this record: %s' % record.id)
     52             return
     53         # forward, reverse = simulate_read(record, ErrorModel, i)

...........................................................................
/usr/local/lib/python2.7/dist-packages/iss/generator.py in simulate_read(record=SeqRecord(seq=Seq('GCCCCTGAATGCGGCTAATCCTAACCATG...ame='PV3Test', description='PV3Test', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, i=5)
    127         id='%s_%s_2' % (header, i),
    128         description=''
    129     )
    130     # add the indels, the qual scores and modify the record accordingly
    131     reverse.seq = ErrorModel.introduce_indels(
--> 132         reverse, 'reverse', sequence, bounds)
        reverse = SeqRecord(seq=Seq('TGTGACACTGAAATCCTGTCTTCAAACAA...me='<unknown name>', description=u'', dbxrefs=[])
        sequence = Seq('GCCCCTGAATGCGGCTAATCCTAACCATGGAGCAGGCAGCTGCAACCCAGCAGC...ACA', SingleLetterAlphabet())
        bounds = (733, 1034)
    133     reverse = ErrorModel.introduce_error_scores(reverse, 'reverse')
    134     reverse.seq = ErrorModel.mut_sequence(reverse, 'reverse')
    135 
    136     return (forward, reverse)

...........................................................................
/usr/local/lib/python2.7/dist-packages/iss/error_models/__init__.py in introduce_indels(self=<iss.error_models.kde.KDErrorModel object>, record=SeqRecord(seq=Seq('TGTGACACTGAAATCCTGTCTTCAAACAA...me='<unknown name>', description=u'', dbxrefs=[]), orientation=u'reverse', full_seq=Seq('GCCCCTGAATGCGGCTAATCCTAACCATGGAGCAGGCAGCTGCAACCCAGCAGC...ACA', SingleLetterAlphabet()), bounds=(733, 1034))
    176                     position += 1
    177                     continue
    178                 for nucl_to_insert, prob in insertions[position].items():
    179                     if random.random() < prob:
    180                         # we want to insert after the base read
--> 181                         mutable_seq.insert(position + 1, nucl_to_insert)
        mutable_seq.insert = <bound method MutableSeq.insert of MutableSeq('T...AGTTAAGGAGTAAAACG...ATC', IUPACUnambiguousDNA())>
        position = 34
        nucl_to_insert = u'T'
    182                 if random.random() < deletions[position][mutable_seq[nucl]]:
    183                     mutable_seq.pop(position)
    184                 position += 1
    185             except IndexError as e:

...........................................................................
/usr/local/lib/python2.7/dist-packages/Bio/Seq.py in insert(self=MutableSeq('TGTGACACTGAAATCCTGTCTTCAAACAATTTCAATAAGTTAAGGAGTAAAACG...ATC', IUPACUnambiguousDNA()), i=35, c=u'T')
   1921         """Add a subsequence to the mutable sequence object."""
   1922         self.data.append(c)
   1923 
   1924     def insert(self, i, c):
   1925         """Add a subsequence to the mutable sequence object at a given index."""
-> 1926         self.data.insert(i, c)
        self.data.insert = <built-in method insert of array.array object>
        i = 35
        c = u'T'
   1927 
   1928     def pop(self, i=(-1)):
   1929         """Remove a subsequence of a single letter at given index."""
   1930         c = self.data[i]

TypeError: array item must be char